This lab will illustrate how to use RMarkdown to create reproducible analyses.

Data-Driven Documents

What are Data-Driven Documents?

Data-driven documents are formats that combine text and analysis (i.e. data and code). By combining everything in a single file, we promote transparency and reproducibility. For any given table, figure, or model in the document, you should be able to easily discern how it was created, from what data, and what analysis was used.

We will use the R Markdown format.

How do Data-Driven Documents Work?

All of the document formats build from a simple text formatting convention called markdown.

To create an R Markdown document, you need three things:

  1. A header to specify the document type
  2. Some text (formatted in markdown)
  3. Some code (inside a “code chunk”)


Knitting R Markdown Files

Code is placed inside of “chunks” in the documents:

When you “knit” a file R Studio will run all of code, embed the output into your document, and then convert the file to whichever type you have specified in the file header.



Output Types

You can select from many different document types, including HTML pages, Microsoft word, presentation formats, or dashboards.


Check out these examples:

R Markdown Formats
R Markdown Gallery



HTML Pages

---
output: html_document
---


Dashboards

---
output: flexdashboard::flex_dashboard:
---

[ dashboard example ] [ source code ] [ blog about the tracker ]


PDFs

---
output: pdf_document
---



Installation

You will need the following programs to generate data-driven documents in R:

When you first try to knit a file, you might get a message that you need the following packages:

  • rmarkdown
  • knitr

These can be installed in the usual manner:

install.packages( "rmarkdown" )
install.packages( "knitr" )

PDFs:

If you would like to knit to PDF you need one additional program. TeX creates publication-quality PDF files. The open-source version is called MiKTeX download page.

If you have problems, you can find some nice tutorials like this one: https://www.reed.edu/data-at-reed/software/R/r_studio_pc.html

Specialized packages:

Some document output formats require specific R packages. For example:

  • journal templates
  • dashboards
  • r websites
  • books in bookdown

You can find many of these packages on the R Markdown templates page.


Working with Markdown

Markdown is a set of simple conventions for formatting text in R Markdown (RMD) files.

It makes it easy to create professional documents with minimal effort.

Here are the basic formatting rules for Markdown:

Headers

# Heading One (h1)

## Heading Two (h2)

### Heading Three (h3)

#### Heading Four (h4)

##### Heading Five (h5)

###### Heading Six (h6)

Text Style

With Markdown, it is possible to emphasize words by making them *italicized*, using *astericks* or _underscores_, or making them **bold**, using **double astericks** or __double underscores__. 

Of course, you can combine those two formats, with both _**bold and italicized**_ text, using any combination of the above syntax. 

You can also add a strikethrough to text using a ~~double tilde~~.

With Markdown, it is possible to emphasize words by making them italicized, using astericks or underscores, or making them bold, using double astericks or double underscores.

Of course, you can combine those two formats, with both bold and italicized text, using any combination of the above syntax.

You can also add a strikethrough to text using a double tilde.

Lists

Unordered

* First item
* Second item
* Third item
    * First nested item
    * Second nested item
  • First item
  • Second item
  • Third item
    • First nested item
    • Second nested item

Ordered

1. First item
2. Second item
3. Third item
    1. First nested item
    2. Second nested item
  1. First item
  2. Second item
  3. Third item
    1. First nested item
    2. Second nested item

Images

Insert images in a similar way, but add an exclamation mark in front of square brackets [ ], and the image file name goes in the parentheses ( ).

![alt_text_here](image_file.png)

The alt text appears when the image cannot be located, or is read by devices for the blind when the mouse hovers over the image. It

Or you can link directly to an image online using the URL address of the image:

![](https://www.rodaw.com/wp-content/uploads/2017/02/Mark-Down-MonsterDogLampShade-1.jpg)

Tables

| Title 1          | Title 2          | Title 3         | Title 4         |
|------------------|------------------|-----------------|-----------------|
| First entry      | Second entry     | Third entry     | Fourth entry    |
| Fifth entry      | Sixth entry      | Seventh entry   | Eight entry     |
| Ninth entry      | Tenth entry      | Eleventh entry  | Twelfth entry   |
| Thirteenth entry | Fourteenth entry | Fifteenth entry | Sixteenth entry |
Title 1 Title 2 Title 3 Title 4
First entry Second entry Third entry Fourth entry
Fifth entry Sixth entry Seventh entry Eight entry
Ninth entry Tenth entry Eleventh entry Twelfth entry
Thirteenth entry Fourteenth entry Fifteenth entry Sixteenth entry

Blockquotes

Single line

> My mom always said life was like a box of chocolates. You never know what you're gonna get.

My mom always said life was like a box of chocolates. You never know what you’re gonna get.

Multiline

> What do you get when you cross an insomniac, an agnostic and a dyslexic?
>
> Someone who stays up all night wondering whether there really is a dog.
>
> – _Hal Incandenza_

What do you get when you cross an insomniac, an agnostic and a dyslexic?

Someone who stays up all night wondering whether there really is a dog.

– Hal Incandenza

Horizontal Rule

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Questions?


Please report any needed corrections to the Issues page. Thanks!



Last updated 26 May, 2023